Should the freedoms of religion and speech be more strictly regulated if this freedom is used for such destructive purposes? If so, who has the power to decide what is acceptable?

Interesting that you single out religion and speech, and not, say, politics and speech or certain types of industry and speech or even treatments of the environment and speech. I believe that there is an assumption in popular culture (perhaps encouraged by Dawkins et al) that religion is more dangerous than, say, secular alternatives. This charge has been effectively challenged by a range of thinkers; I especially recommend Keith Ward's book, Is Religion Dangerous?

In any case, there are various reasons why the state may, even in a liberal, pluralistic democracy, regulate speech, religion, political viewpoints, industries, etc, in light of the wrongful infliction of harm or risk of harm and offense. Probably the best work on this is Joel Feinberg's awesome four volume work on The Moral Limits of the Criminal Law (Oxford University Press). The book is full of real and imagined cases that test current and future laws. Even if you disagree with him, Feinberg (who, sadly, died in 2004) has been a brilliant contributor to the debate that involves your question.